MEERCAT: Multiplexed Efficient Cell Free Expression of Recombinant QconCATs For Large Scale Absolute Proteome Quantification

Takemori, Nobuaki, Takemori, Ayako, Tanaka, Yuki, Endo, Yaeta, Hurst, Jane L ORCID: 0000-0002-3728-9624, Gomez-Baena, Guadalupe ORCID: 0000-0003-3796-3874, Harman, Victoria M ORCID: 0000-0002-0990-153X and Beynon, Robert J ORCID: 0000-0003-0857-495X
(2017) MEERCAT: Multiplexed Efficient Cell Free Expression of Recombinant QconCATs For Large Scale Absolute Proteome Quantification. Molecular and Cellular Proteomics, 16 (12). pp. 2169-2183.

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A major challenge in proteomics is the absolute accurate quantification of large numbers of proteins. QconCATs, artificial proteins that are concatenations of multiple standard peptides, are well established as an efficient means to generate standards for proteome quantification. Previously, QconCATs have been expressed in bacteria, but we now describe QconCAT expression in a robust, cell-free system. The new expression approach rescues QconCATs that previously were unable to be expressed in bacteria and can reduce the incidence of proteolytic damage to QconCATs. Moreover, it is possible to cosynthesize QconCATs in a highly-multiplexed translation reaction, coexpressing tens or hundreds of QconCATs simultaneously. By obviating bacterial culture and through the gain of high level multiplexing, it is now possible to generate tens of thousands of standard peptides in a matter of weeks, rendering absolute quantification of a complex proteome highly achievable in a reproducible, broadly deployable system. One of the major challenges in proteomics is absolute quantification of individual proteins. The predominant technology in large scale protein quantification is MS of (usually tryptic) peptides derived from proteolysis of the proteome in vitro and it is well understood that although mass spectrometers can deliver linearity of response over many orders of magnitude, the response factor (signal intensity per mol of peptide) varies considerably among individual peptides (1, 2). One outcome is that commonly used “label-free” methods that sum the precursor ion intensities for the peptides derived from a single protein, are excellent for relative quantification, but are less satisfactory for absolute quantification. MS-based absolute quantification of proteins can be supported by external standards that are analyzed before and/or after the analyte or by stable-isotope labeled internal standards that are coanalyzed and which define the response factor for each peptide (3). These peptides can be individually synthesized and quantified (4) and there have been some remarkable large-scale studies. However, large numbers of accurately quantified peptides are costly. Further, a commercially produced, accurately quantified standard peptide is a finite resource and is hence best focused on low numbers of assays of a small number of target proteins. Intact protein standards (5⇓–7), or large fragments (8) provide multiple potential peptides for quantification of the targets. In 2005, a novel approach to the creation of standard peptides by biosynthesis was proposed in the form of QconCATs (9⇓⇓⇓–13). QconCATs are artificial proteins that are concatenations of standard peptides from multiple natural proteins, sometimes interspersed by short peptides to recapitulate the primary sequence context of the natural counterpart (14, 15). Peptides suitable for quantification are referred to as Q-peptides, and are not synonymous with proteotypic peptides, as the latter term refers to peptides, unique to one protein, that drive protein identification, not quantification. QconCATs genes are synthesized de novo and are routinely expressed in E. coli cultured in media supplemented with appropriate stable isotope labeled amino acids, such that peptides derived from QconCATs are discriminable from natural peptides within the mass spectrometer. The purified QconCATs are mixed with the biological analyte sample and coproteolyzed to generate a mixture of labeled (standard) and unlabeled (analyte) peptide pairs that can be analyzed by liquid chromatography coupled to MS to yield absolute quantification of the analyte proteins. QconCATs have the added advantage that with appropriate control of proteolysis (11) all standards are, by definition, in a 1:1 ratio, rendering independent quantification of each standard unnecessary; a single common peptide can function to quantify the QconCAT (13). However, successful expression of novel QconCATs in E. coli is not always guaranteed. In a large-scale quantification project that used over 100 independently designed and expressed QconCATs, we discovered that ∼1 in 10 of the concatamers would fail to express, even when a range of expression conditions were explored. Further, at a low frequency, some QconCATs were prone to proteolysis in the bacterial cell or during purification, rendering them of reduced value for quantification. Effective QconCAT deployment across large scale proteome quantification studies would require a high level of confidence in expression of every new construct. In addition, living-cell based synthesis systems are not ideal for high-throughput preparation of multiple QconCATs and many mass spectrometry laboratories are not equipped for the basic molecular biology that would be needed to subclone and express recombinant proteins. To enhance the potential of QconCAT technology for large-scale proteome quantification, we here focus on a wheat germ cell-free protein synthesis system (WGCFS)1 as a major enhancement to the workflow of high throughput QconCAT synthesis. WGCFS, which uses the powerful translation system for germination stored in wheat germ, realizes the highest yield of translation among commercially available eukaryotic derived cell-free systems (16⇓⇓⇓–20). Using WGCFS, we previously demonstrated the feasibility of synthesis of single, small QconCATs, typically 25 kDa (21). In the present study, we first assessed whether WGCFS could be used to express more typical QconCATs at approx. 60 kDa (for quantification of ∼25 proteins at two peptides per target protein), whether WGCFS would rescue “failed” QconCATs and whether this cell free system was able to reduce the risk of proteolytic degradation. Further, we established whether an additional step in efficiency could be derived from coexpression of multiple QconCATs in a single WGCFS reaction.

Item Type: Article
Uncontrolled Keywords: Cell-Free System, Humans, Peptides, Proteome, Isotope Labeling, Proteomics, Base Sequence, Gene Library, Tandem Mass Spectrometry
Depositing User: Symplectic Admin
Date Deposited: 31 Jan 2018 07:47
Last Modified: 19 Jan 2023 06:42
DOI: 10.1074/mcp.RA117.000284
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